BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716888.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 3,386,932 number of mapped reads = 3,143,488 (92.81%) number of supplementary alignments = 16,895 (0.5%) number of secondary alignments = 0 number of mapped bases = 183,838,197 bp number of sequenced bases = 183,786,854 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 183,228 duplication rate = 4.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7509 >>>>>>> ACTG content number of A's = 47,482,751 bp (25.84%) number of C's = 37,712,657 bp (20.52%) number of T's = 55,730,634 bp (30.32%) number of G's = 42,855,605 bp (23.32%) number of N's = 5,207 bp (0%) GC percentage = 43.84% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 890,352 number of insertions = 10,369 mapped reads with insertion percentage = 0.33% number of deletions = 32,603 mapped reads with deletion percentage = 1.03% homopolymer indels = 45.71% >>>>>>> Coverage mean coverageData = 0.0594X std coverageData = 0.5603X There is a 4.91% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 18606061 0.07464800258210791 1.2827671744113676 chr2 243199373 17240824 0.07089172882036994 0.6542937071093129 chr3 198022430 12485367 0.06305026657838711 0.29584288249638807 chr4 191154276 8342088 0.04364060367658216 0.27166110609719174 chr5 180915260 7965995 0.044031636690017195 0.2558230079484562 chr6 171115067 12524880 0.07319565845128062 0.3854034890689819 chr7 159138663 13436301 0.08443140558495203 0.8153719709197609 chr8 146364022 10494255 0.0716996899688914 0.4120988904109781 chr9 141213431 7497623 0.053094262683837774 0.4267444045333039 chr10 135534747 9706066 0.07161311925420867 0.4908483745149146 chr11 135006516 5993147 0.04439153884987299 0.3844187413420984 chr12 133851895 7320585 0.05469167993475176 0.28762759605418464 chr13 115169878 4054661 0.03520591556066422 0.2203846796565428 chr14 107349540 3943754 0.036737502554738476 0.2677263341301483 chr15 102531392 5360437 0.05228093460391136 0.2714503960210236 chr16 90354753 3762918 0.041646043789196126 0.27835587901203734 chr17 81195210 3895790 0.04798053973873582 0.27735867181096546 chr18 78077248 6401844 0.08199371986061804 0.8388175206886961 chr19 59128983 4503834 0.07616965101530665 0.801964255463832 chr20 63025520 2741870 0.043504123409057155 0.2518200235868517 chr21 48129895 2312109 0.04803893713044668 0.29031806184317527 chr22 51304566 2834509 0.055248669289980935 0.2768588731775346 chrMT 16571 183960 11.101321585903083 6.353260754722189 chrX 155270560 11800172 0.07599748464873186 0.4003669333793638 chrY 59373566 429147 0.007227913512892253 0.15801265708020074